Starting phenix.real_space_refine on Sun Mar 24 19:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0y_11972/03_2024/7b0y_11972.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 274 5.49 5 Mg 1 5.21 5 S 242 5.16 5 C 26605 2.51 5 N 7734 2.21 5 O 8928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 611": "OD1" <-> "OD2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A ASP 894": "OD1" <-> "OD2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1241": "OD1" <-> "OD2" Residue "A ASP 1249": "OD1" <-> "OD2" Residue "A ASP 1250": "OD1" <-> "OD2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1258": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "A ASP 1449": "OD1" <-> "OD2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "A ASP 1476": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "B ASP 492": "OD1" <-> "OD2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B ASP 850": "OD1" <-> "OD2" Residue "B ASP 863": "OD1" <-> "OD2" Residue "B TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 905": "OD1" <-> "OD2" Residue "B PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1057": "OD1" <-> "OD2" Residue "B ASP 1081": "OD1" <-> "OD2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ASP 127": "OD1" <-> "OD2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G ASP 153": "OD1" <-> "OD2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H ASP 128": "OD1" <-> "OD2" Residue "H ASP 138": "OD1" <-> "OD2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "b GLU 49": "OE1" <-> "OE2" Residue "b ASP 50": "OD1" <-> "OD2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b GLU 64": "OE1" <-> "OE2" Residue "b TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 154": "OE1" <-> "OE2" Residue "b ASP 170": "OD1" <-> "OD2" Residue "b ARG 188": "NH1" <-> "NH2" Residue "c GLU 25": "OE1" <-> "OE2" Residue "c TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 42": "OD1" <-> "OD2" Residue "c PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 79": "OD1" <-> "OD2" Residue "c ASP 92": "OD1" <-> "OD2" Residue "c PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "e GLU 21": "OE1" <-> "OE2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e GLU 72": "OE1" <-> "OE2" Residue "e TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "f TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "g PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 60": "OD1" <-> "OD2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g ARG 76": "NH1" <-> "NH2" Residue "h PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 44": "OE1" <-> "OE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i ASP 37": "OD1" <-> "OD2" Residue "i ARG 51": "NH1" <-> "NH2" Residue "i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 23": "OD1" <-> "OD2" Residue "j PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 46": "OD1" <-> "OD2" Residue "j ASP 89": "OD1" <-> "OD2" Residue "k PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 33": "OD1" <-> "OD2" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k ARG 61": "NH1" <-> "NH2" Residue "k ARG 66": "NH1" <-> "NH2" Residue "k TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k ASP 77": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43792 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11263 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9052 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1030 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 769 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 774 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "a" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3485 Classifications: {'RNA': 164} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 15, 'rna3p_pur': 67, 'rna3p_pyr': 70} Link IDs: {'rna2p': 27, 'rna3p': 136} Chain: "b" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1543 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 12, 'TRANS': 173} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "e" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "f" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "g" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "h" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "i" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "j" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "k" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 121.625 108.245 136.583 1.00 51.93 S ATOM 486 SG CYS A 74 121.156 112.528 136.060 1.00 48.48 S ATOM 533 SG CYS A 81 122.661 111.003 133.410 1.00 43.07 S ATOM 768 SG CYS A 111 165.708 103.396 153.093 1.00 61.14 S ATOM 796 SG CYS A 114 164.364 105.356 155.585 1.00 62.99 S ATOM 1109 SG CYS A 154 167.653 105.849 154.604 1.00 75.39 S ATOM 19885 SG CYS B1119 132.711 121.317 145.561 1.00 43.18 S ATOM 19907 SG CYS B1122 135.338 118.427 144.010 1.00 38.64 S ATOM 20022 SG CYS B1137 132.076 117.264 144.602 1.00 46.96 S ATOM 20043 SG CYS B1140 135.036 119.073 147.640 1.00 46.76 S ATOM 21009 SG CYS C 88 93.425 125.848 76.296 1.00 43.12 S ATOM 21022 SG CYS C 90 93.300 122.912 78.134 1.00 46.46 S ATOM 21057 SG CYS C 94 92.708 122.207 74.851 1.00 36.10 S ATOM 21079 SG CYS C 97 96.127 122.281 75.959 1.00 34.90 S ATOM 28417 SG CYS I 17 200.561 72.155 107.265 1.00 54.81 S ATOM 28441 SG CYS I 20 197.107 72.233 109.316 1.00 52.49 S ATOM 28602 SG CYS I 39 198.594 75.060 110.780 1.00 60.21 S ATOM 28627 SG CYS I 42 200.678 72.054 110.874 1.00 59.96 S ATOM 28979 SG CYS I 86 194.125 91.429 68.090 1.00 43.53 S ATOM 29003 SG CYS I 89 193.282 89.143 65.661 1.00 45.83 S ATOM 29207 SG CYS I 114 190.258 90.244 67.460 1.00 40.47 S ATOM 29242 SG CYS I 119 193.218 87.817 69.070 1.00 44.95 S ATOM 29352 SG CYS J 7 124.924 117.101 64.832 1.00 23.73 S ATOM 29376 SG CYS J 10 122.597 119.765 62.641 1.00 22.22 S ATOM 29640 SG CYS J 44 126.721 119.647 62.296 1.00 23.78 S ATOM 29646 SG CYS J 45 124.333 117.602 60.640 1.00 21.96 S ATOM 30808 SG CYS L 19 112.037 81.547 85.739 1.00 44.71 S ATOM 30827 SG CYS L 22 109.360 80.018 83.759 1.00 47.16 S ATOM 30944 SG CYS L 36 108.540 79.262 87.214 1.00 55.49 S ATOM 30970 SG CYS L 39 111.467 78.234 85.726 1.00 59.79 S Time building chain proxies: 23.48, per 1000 atoms: 0.54 Number of scatterers: 43792 At special positions: 0 Unit cell: (234.15, 197.4, 203.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 242 16.00 P 274 15.00 Mg 1 11.99 O 8928 8.00 N 7734 7.00 C 26605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.80 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 39 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8916 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 58 sheets defined 35.2% alpha, 21.5% beta 77 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 15.26 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.622A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.853A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.606A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.519A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.576A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.526A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.984A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.769A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.643A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.648A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 490' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.560A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.172A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.623A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.588A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.687A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.729A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.532A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.566A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.511A pdb=" N LEU A1127 " --> pdb=" O ARG A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.797A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.920A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.559A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.296A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.769A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.707A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.310A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.831A pdb=" N PHE B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.319A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.627A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.741A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.595A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.866A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.849A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.575A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.328A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.891A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.671A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.803A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.816A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.903A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.522A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.614A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 90 removed outlier: 4.124A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.561A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.515A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.582A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.577A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'b' and resid 64 through 89 removed outlier: 3.990A pdb=" N GLU b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR b 84 " --> pdb=" O GLN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 124 Processing helix chain 'b' and resid 153 through 165 removed outlier: 3.583A pdb=" N MET b 157 " --> pdb=" O HIS b 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS b 158 " --> pdb=" O GLU b 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA b 160 " --> pdb=" O ASP b 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS b 162 " --> pdb=" O HIS b 158 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS b 163 " --> pdb=" O SER b 159 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP b 165 " --> pdb=" O TYR b 161 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 193 Processing helix chain 'c' and resid 22 through 35 Processing helix chain 'c' and resid 36 through 38 No H-bonds generated for 'chain 'c' and resid 36 through 38' Processing helix chain 'c' and resid 61 through 73 Processing helix chain 'c' and resid 91 through 99 Processing helix chain 'e' and resid 18 through 27 Processing helix chain 'e' and resid 29 through 39 removed outlier: 3.870A pdb=" N THR e 33 " --> pdb=" O LEU e 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 14 Processing helix chain 'g' and resid 16 through 28 Processing helix chain 'i' and resid 4 through 13 Processing helix chain 'i' and resid 74 through 80 Processing helix chain 'j' and resid 7 through 11 Processing helix chain 'k' and resid 3 through 8 removed outlier: 3.698A pdb=" N LEU k 7 " --> pdb=" O LEU k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.669A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 94 removed outlier: 11.210A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.207A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.646A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 4.160A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 477 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.054A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.690A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.406A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.406A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.800A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 3.500A pdb=" N GLN A 888 " --> pdb=" O VAL A 879 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.728A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.532A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 4.785A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC4, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.696A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.780A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AD2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.309A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.571A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.571A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.351A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE1, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.670A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AE4, first strand: chain 'C' and resid 8 through 9 removed outlier: 5.995A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.560A pdb=" N LEU C 103 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.708A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.546A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.546A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.459A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.772A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AF4, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.895A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 127 through 129 Processing sheet with id=AF6, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.512A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF9, first strand: chain 'b' and resid 129 through 136 removed outlier: 5.348A pdb=" N TYR b 146 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA b 108 " --> pdb=" O LEU b 175 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU b 175 " --> pdb=" O ALA b 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 168 through 169 Processing sheet with id=AG2, first strand: chain 'c' and resid 40 through 46 removed outlier: 6.922A pdb=" N ILE c 58 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE c 43 " --> pdb=" O PHE c 56 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE c 56 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL c 45 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLN c 54 " --> pdb=" O VAL c 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 55 through 57 removed outlier: 3.753A pdb=" N ALA i 56 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL i 48 " --> pdb=" O ALA i 56 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN i 60 " --> pdb=" O ALA h 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET h 69 " --> pdb=" O LYS h 20 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN h 28 " --> pdb=" O CYS h 45 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS h 45 " --> pdb=" O GLN h 28 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL h 41 " --> pdb=" O ARG h 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU h 44 " --> pdb=" O GLY h 58 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLY h 58 " --> pdb=" O GLU h 44 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL h 46 " --> pdb=" O ASN h 56 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN h 56 " --> pdb=" O VAL h 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL h 61 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU g 86 " --> pdb=" O TRP g 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU g 35 " --> pdb=" O MET g 41 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET g 41 " --> pdb=" O LEU g 35 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN g 40 " --> pdb=" O HIS g 65 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS g 65 " --> pdb=" O ASN g 40 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG g 42 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU g 63 " --> pdb=" O ARG g 42 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU g 44 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA g 61 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS g 46 " --> pdb=" O ASP g 59 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL g 57 " --> pdb=" O ILE g 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP g 60 " --> pdb=" O GLY g 75 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY g 75 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU g 62 " --> pdb=" O GLN g 73 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN g 73 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG g 76 " --> pdb=" O GLY f 74 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY f 74 " --> pdb=" O ARG g 76 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU f 28 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU f 49 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS f 30 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR f 47 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN f 43 " --> pdb=" O VAL f 34 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN f 43 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL f 62 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA f 45 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY f 60 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR f 47 " --> pdb=" O HIS f 58 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS f 58 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU f 49 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU f 61 " --> pdb=" O ARG e 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG e 111 " --> pdb=" O GLU f 61 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN e 45 " --> pdb=" O ILE e 107 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL e 109 " --> pdb=" O LEU e 43 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU e 43 " --> pdb=" O VAL e 109 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG e 55 " --> pdb=" O ASN e 69 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASN e 69 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL e 66 " --> pdb=" O PHE e 100 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE e 100 " --> pdb=" O VAL e 66 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU e 68 " --> pdb=" O LYS e 98 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS e 98 " --> pdb=" O GLU e 68 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU k 18 " --> pdb=" O ARG k 66 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE k 68 " --> pdb=" O THR k 16 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR k 16 " --> pdb=" O PHE k 68 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL k 25 " --> pdb=" O MET k 45 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET k 45 " --> pdb=" O VAL k 25 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY k 27 " --> pdb=" O VAL k 43 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL k 43 " --> pdb=" O GLY k 27 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE k 29 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS k 41 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS k 39 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER k 59 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS k 41 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR k 57 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 13.565A pdb=" N LEU k 55 " --> pdb=" O GLY j 84 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N GLY j 84 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR k 57 " --> pdb=" O VAL j 82 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL j 82 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER j 79 " --> pdb=" O ILE j 20 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ARG j 16 " --> pdb=" O GLU j 83 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE j 26 " --> pdb=" O GLU j 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU j 47 " --> pdb=" O ILE j 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE j 28 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS j 45 " --> pdb=" O ILE j 28 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY j 68 " --> pdb=" O ASP j 44 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP j 46 " --> pdb=" O VAL j 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL j 66 " --> pdb=" O ASP j 46 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU j 69 " --> pdb=" O LEU i 73 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU i 21 " --> pdb=" O ARG i 69 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU i 71 " --> pdb=" O THR i 19 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR i 19 " --> pdb=" O LEU i 71 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU i 73 " --> pdb=" O ILE i 17 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE i 17 " --> pdb=" O LEU i 73 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL i 27 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL i 48 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG i 29 " --> pdb=" O ILE i 46 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE i 46 " --> pdb=" O ARG i 29 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN i 42 " --> pdb=" O ILE i 33 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 50 through 51 removed outlier: 3.686A pdb=" N ILE j 51 " --> pdb=" O ARG j 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG j 61 " --> pdb=" O ILE j 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 1534 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 376 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 27.40 Time building geometry restraints manager: 20.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13396 1.34 - 1.45: 7591 1.45 - 1.57: 23246 1.57 - 1.69: 544 1.69 - 1.81: 391 Bond restraints: 45168 Sorted by residual: bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" C ASP H 16 " pdb=" O ASP H 16 " ideal model delta sigma weight residual 1.238 1.222 0.016 1.28e-02 6.10e+03 1.51e+00 bond pdb=" CA VAL A1121 " pdb=" CB VAL A1121 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.26e+00 ... (remaining 45163 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 2691 106.42 - 113.31: 24794 113.31 - 120.20: 15920 120.20 - 127.09: 17932 127.09 - 133.97: 919 Bond angle restraints: 62256 Sorted by residual: angle pdb=" C3' U a 90 " pdb=" O3' U a 90 " pdb=" P G a 91 " ideal model delta sigma weight residual 120.20 124.68 -4.48 1.50e+00 4.44e-01 8.91e+00 angle pdb=" CA LYS c 22 " pdb=" CB LYS c 22 " pdb=" CG LYS c 22 " ideal model delta sigma weight residual 114.10 108.52 5.58 2.00e+00 2.50e-01 7.79e+00 angle pdb=" O3' U a 90 " pdb=" C3' U a 90 " pdb=" C2' U a 90 " ideal model delta sigma weight residual 109.50 113.61 -4.11 1.50e+00 4.44e-01 7.52e+00 angle pdb=" N ASN G 124 " pdb=" CA ASN G 124 " pdb=" C ASN G 124 " ideal model delta sigma weight residual 112.55 109.18 3.37 1.35e+00 5.49e-01 6.22e+00 angle pdb=" N ILE C 39 " pdb=" CA ILE C 39 " pdb=" C ILE C 39 " ideal model delta sigma weight residual 112.96 110.51 2.45 1.00e+00 1.00e+00 6.02e+00 ... (remaining 62251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 26631 35.96 - 71.92: 980 71.92 - 107.88: 99 107.88 - 143.84: 3 143.84 - 179.80: 10 Dihedral angle restraints: 27723 sinusoidal: 13938 harmonic: 13785 Sorted by residual: dihedral pdb=" O4' U a 115 " pdb=" C1' U a 115 " pdb=" N1 U a 115 " pdb=" C2 U a 115 " ideal model delta sinusoidal sigma weight residual 200.00 41.90 158.10 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" C4' DT N 22 " pdb=" C3' DT N 22 " pdb=" O3' DT N 22 " pdb=" P DT N 23 " ideal model delta sinusoidal sigma weight residual -140.00 39.80 -179.80 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' G P 135 " pdb=" C3' G P 135 " pdb=" O3' G P 135 " pdb=" P G P 136 " ideal model delta sinusoidal sigma weight residual -110.00 69.67 -179.67 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 27720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 5385 0.034 - 0.069: 1071 0.069 - 0.103: 419 0.103 - 0.138: 223 0.138 - 0.172: 5 Chirality restraints: 7103 Sorted by residual: chirality pdb=" CA HIS k 12 " pdb=" N HIS k 12 " pdb=" C HIS k 12 " pdb=" CB HIS k 12 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL c 57 " pdb=" N VAL c 57 " pdb=" C VAL c 57 " pdb=" CB VAL c 57 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" C3' U a 90 " pdb=" C4' U a 90 " pdb=" O3' U a 90 " pdb=" C2' U a 90 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 7100 not shown) Planarity restraints: 7060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE c 75 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO c 76 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO c 76 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO c 76 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 78 " -0.004 2.00e-02 2.50e+03 8.45e-03 1.43e+00 pdb=" CG TYR c 78 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR c 78 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR c 78 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR c 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 78 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR c 78 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR c 78 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO b 55 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO b 56 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO b 56 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO b 56 " 0.016 5.00e-02 4.00e+02 ... (remaining 7057 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 356 2.54 - 3.13: 34656 3.13 - 3.72: 68992 3.72 - 4.31: 100552 4.31 - 4.90: 162621 Nonbonded interactions: 367177 Sorted by model distance: nonbonded pdb=" O2' U a 90 " pdb=" OP2 G a 91 " model vdw 1.954 2.440 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 1.976 2.440 nonbonded pdb=" O2' G a 15 " pdb=" OP1 G a 16 " model vdw 2.001 2.440 nonbonded pdb=" OG1 THR B 565 " pdb=" O ARG B 610 " model vdw 2.003 2.440 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.020 2.170 ... (remaining 367172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.220 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 143.230 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45168 Z= 0.126 Angle : 0.423 6.262 62256 Z= 0.242 Chirality : 0.038 0.172 7103 Planarity : 0.002 0.058 7060 Dihedral : 17.189 179.804 18807 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.02 % Allowed : 0.95 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.11), residues: 4687 helix: -2.05 (0.11), residues: 1409 sheet: -2.09 (0.16), residues: 781 loop : -1.81 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 49 HIS 0.006 0.000 HIS k 39 PHE 0.007 0.001 PHE j 48 TYR 0.011 0.001 TYR c 78 ARG 0.011 0.000 ARG c 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 771 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 ASP cc_start: 0.7104 (t0) cc_final: 0.6795 (t0) REVERT: A 1130 ILE cc_start: 0.8282 (mp) cc_final: 0.7974 (mm) REVERT: A 1289 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 1351 ASP cc_start: 0.6911 (m-30) cc_final: 0.6674 (m-30) REVERT: A 1412 MET cc_start: 0.8090 (tmm) cc_final: 0.7845 (tmm) REVERT: A 1414 ILE cc_start: 0.8748 (mm) cc_final: 0.8390 (mm) REVERT: B 146 LYS cc_start: 0.8257 (mttm) cc_final: 0.8013 (mttp) REVERT: B 262 TYR cc_start: 0.8445 (m-10) cc_final: 0.8106 (m-80) REVERT: B 677 MET cc_start: 0.9005 (tpp) cc_final: 0.8181 (tpp) REVERT: B 934 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8573 (mtpt) REVERT: B 1039 SER cc_start: 0.8645 (t) cc_final: 0.8405 (p) REVERT: C 48 ASP cc_start: 0.7394 (t70) cc_final: 0.7106 (t0) REVERT: C 186 TYR cc_start: 0.8553 (p90) cc_final: 0.8038 (p90) REVERT: E 61 LEU cc_start: 0.8468 (tp) cc_final: 0.8155 (tp) REVERT: F 115 TYR cc_start: 0.8096 (p90) cc_final: 0.7721 (p90) REVERT: G 104 MET cc_start: 0.0040 (mmp) cc_final: -0.0181 (mmp) REVERT: I 25 TYR cc_start: 0.8159 (m-80) cc_final: 0.7483 (m-80) REVERT: I 51 SER cc_start: 0.7967 (t) cc_final: 0.7294 (p) REVERT: I 54 TYR cc_start: 0.8208 (t80) cc_final: 0.8003 (t80) REVERT: J 50 LEU cc_start: 0.8532 (tp) cc_final: 0.8282 (tt) REVERT: J 58 LYS cc_start: 0.8560 (mttt) cc_final: 0.8270 (mtpp) REVERT: K 17 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8009 (mtmm) REVERT: b 158 HIS cc_start: 0.7843 (m90) cc_final: 0.7577 (m90) REVERT: g 41 MET cc_start: 0.3200 (mtt) cc_final: 0.2934 (ptp) REVERT: k 8 MET cc_start: 0.4463 (mpp) cc_final: 0.4194 (mmt) REVERT: k 36 MET cc_start: 0.0674 (ttm) cc_final: -0.0179 (mpp) REVERT: k 45 MET cc_start: -0.0369 (ttp) cc_final: -0.0798 (tpt) outliers start: 1 outliers final: 1 residues processed: 772 average time/residue: 0.6236 time to fit residues: 762.2391 Evaluate side-chains 450 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 384 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 285 optimal weight: 0.0020 chunk 444 optimal weight: 50.0000 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 370 HIS B 430 ASN B1030 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 210 HIS c 10 HIS c 39 GLN g 19 ASN h 26 HIS j 55 ASN j 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 45168 Z= 0.295 Angle : 0.602 10.621 62256 Z= 0.308 Chirality : 0.044 0.196 7103 Planarity : 0.004 0.039 7060 Dihedral : 17.868 178.608 9096 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.85 % Allowed : 9.31 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4687 helix: 0.04 (0.13), residues: 1446 sheet: -1.64 (0.16), residues: 790 loop : -1.14 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 203 HIS 0.005 0.001 HIS B 695 PHE 0.023 0.002 PHE b 106 TYR 0.019 0.002 TYR b 161 ARG 0.010 0.001 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 468 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 GLN cc_start: 0.7429 (mp10) cc_final: 0.7224 (mp10) REVERT: A 520 MET cc_start: 0.8352 (mmm) cc_final: 0.8079 (mmm) REVERT: A 556 GLU cc_start: 0.7306 (mp0) cc_final: 0.6439 (mp0) REVERT: A 593 SER cc_start: 0.8690 (m) cc_final: 0.8405 (p) REVERT: A 923 ASP cc_start: 0.7939 (t0) cc_final: 0.7692 (p0) REVERT: A 1257 LEU cc_start: 0.8024 (pt) cc_final: 0.7798 (pt) REVERT: A 1294 THR cc_start: 0.8709 (m) cc_final: 0.8471 (p) REVERT: A 1344 MET cc_start: 0.7895 (mmm) cc_final: 0.7311 (mtt) REVERT: A 1351 ASP cc_start: 0.7091 (m-30) cc_final: 0.6603 (m-30) REVERT: A 1412 MET cc_start: 0.8362 (tmm) cc_final: 0.8055 (tmm) REVERT: B 262 TYR cc_start: 0.8467 (m-10) cc_final: 0.8077 (m-80) REVERT: B 289 ILE cc_start: 0.8511 (mt) cc_final: 0.8297 (mt) REVERT: B 438 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7068 (ptm-80) REVERT: B 456 GLN cc_start: 0.7693 (tt0) cc_final: 0.7304 (tt0) REVERT: C 48 ASP cc_start: 0.7897 (t70) cc_final: 0.7571 (t0) REVERT: C 186 TYR cc_start: 0.8644 (p90) cc_final: 0.8183 (p90) REVERT: E 61 LEU cc_start: 0.8632 (tp) cc_final: 0.8421 (tp) REVERT: F 107 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.7829 (tpp80) REVERT: F 115 TYR cc_start: 0.8043 (p90) cc_final: 0.7841 (p90) REVERT: G 104 MET cc_start: 0.0661 (mmp) cc_final: 0.0437 (mmp) REVERT: I 51 SER cc_start: 0.8032 (t) cc_final: 0.7743 (p) REVERT: I 54 TYR cc_start: 0.8306 (t80) cc_final: 0.7833 (t80) REVERT: K 110 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7952 (mtmt) REVERT: L 50 LYS cc_start: 0.8497 (mmpt) cc_final: 0.8291 (mmtt) REVERT: b 158 HIS cc_start: 0.8008 (m90) cc_final: 0.7807 (m-70) REVERT: f 27 MET cc_start: 0.1358 (mpp) cc_final: 0.1156 (mpp) REVERT: g 41 MET cc_start: 0.3385 (mtt) cc_final: 0.3121 (ptp) REVERT: g 54 MET cc_start: -0.1870 (ttp) cc_final: -0.2204 (mtp) outliers start: 78 outliers final: 45 residues processed: 512 average time/residue: 0.5525 time to fit residues: 465.8394 Evaluate side-chains 433 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 388 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 63 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 370 optimal weight: 0.1980 chunk 303 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 445 optimal weight: 0.5980 chunk 481 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 chunk 442 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 387 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 552 ASN B 825 GLN B1145 GLN C 66 HIS E 35 GLN E 95 GLN K 29 ASN ** b 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45168 Z= 0.239 Angle : 0.543 8.042 62256 Z= 0.277 Chirality : 0.042 0.244 7103 Planarity : 0.004 0.039 7060 Dihedral : 17.975 179.142 9093 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 11.26 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4687 helix: 0.64 (0.14), residues: 1453 sheet: -1.47 (0.17), residues: 796 loop : -0.88 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1192 HIS 0.006 0.001 HIS b 210 PHE 0.022 0.001 PHE b 106 TYR 0.019 0.001 TYR B 388 ARG 0.009 0.000 ARG b 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 424 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: A 556 GLU cc_start: 0.7361 (mp0) cc_final: 0.6980 (mp0) REVERT: A 593 SER cc_start: 0.8660 (m) cc_final: 0.8374 (p) REVERT: A 711 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 1351 ASP cc_start: 0.7166 (m-30) cc_final: 0.6645 (m-30) REVERT: A 1412 MET cc_start: 0.8410 (tmm) cc_final: 0.7986 (tmm) REVERT: A 1423 ASP cc_start: 0.6637 (t0) cc_final: 0.6108 (t0) REVERT: A 1428 MET cc_start: 0.7589 (mtp) cc_final: 0.7362 (mtp) REVERT: B 93 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7847 (tp) REVERT: B 108 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7721 (ttm) REVERT: B 456 GLN cc_start: 0.7637 (tt0) cc_final: 0.7228 (tt0) REVERT: B 494 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8008 (tmtt) REVERT: B 847 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8617 (ttmt) REVERT: C 48 ASP cc_start: 0.7870 (t70) cc_final: 0.7603 (t0) REVERT: C 186 TYR cc_start: 0.8636 (p90) cc_final: 0.8165 (p90) REVERT: E 61 LEU cc_start: 0.8599 (tp) cc_final: 0.8372 (tp) REVERT: F 107 ARG cc_start: 0.8875 (ttm-80) cc_final: 0.7756 (tpp80) REVERT: G 104 MET cc_start: 0.1090 (mmp) cc_final: 0.0697 (mmp) REVERT: I 51 SER cc_start: 0.8034 (t) cc_final: 0.7703 (p) REVERT: I 54 TYR cc_start: 0.8271 (t80) cc_final: 0.7846 (t80) REVERT: I 111 TYR cc_start: 0.8054 (m-80) cc_final: 0.7837 (m-80) REVERT: L 50 LYS cc_start: 0.8535 (mmpt) cc_final: 0.8308 (mmtt) REVERT: b 67 MET cc_start: 0.4829 (ptm) cc_final: 0.4568 (ptp) REVERT: f 42 MET cc_start: 0.1953 (OUTLIER) cc_final: 0.1690 (mpp) REVERT: g 41 MET cc_start: 0.3355 (mtt) cc_final: 0.3042 (ptp) REVERT: g 54 MET cc_start: -0.1607 (ttp) cc_final: -0.1984 (mtp) REVERT: i 39 MET cc_start: 0.0098 (tpt) cc_final: -0.0163 (tpp) REVERT: i 43 MET cc_start: 0.5867 (mmm) cc_final: 0.5467 (tpp) outliers start: 91 outliers final: 53 residues processed: 482 average time/residue: 0.5615 time to fit residues: 452.7526 Evaluate side-chains 432 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 375 time to evaluate : 4.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain g residue 78 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 50.0000 chunk 335 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 299 optimal weight: 0.1980 chunk 447 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 chunk 233 optimal weight: 0.0980 chunk 424 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 330 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B1030 ASN B1129 ASN H 29 HIS H 131 ASN K 29 ASN K 89 ASN b 158 HIS b 210 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 45168 Z= 0.274 Angle : 0.551 9.989 62256 Z= 0.281 Chirality : 0.042 0.193 7103 Planarity : 0.004 0.041 7060 Dihedral : 18.047 178.967 9093 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.38 % Allowed : 12.92 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4687 helix: 0.85 (0.14), residues: 1447 sheet: -1.41 (0.17), residues: 759 loop : -0.77 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 22 HIS 0.004 0.001 HIS A 685 PHE 0.022 0.001 PHE b 106 TYR 0.023 0.001 TYR B 262 ARG 0.007 0.000 ARG b 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 413 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7753 (pm20) cc_final: 0.7430 (pm20) REVERT: A 524 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: A 593 SER cc_start: 0.8685 (m) cc_final: 0.8451 (p) REVERT: A 711 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 1351 ASP cc_start: 0.7173 (m-30) cc_final: 0.6664 (m-30) REVERT: A 1412 MET cc_start: 0.8375 (tmm) cc_final: 0.7923 (tmm) REVERT: B 93 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 124 LEU cc_start: 0.8331 (tp) cc_final: 0.8113 (tp) REVERT: B 187 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8770 (mm) REVERT: B 456 GLN cc_start: 0.7710 (tt0) cc_final: 0.7299 (tt0) REVERT: B 494 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8119 (tmtt) REVERT: B 554 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 847 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8594 (ttmt) REVERT: B 1070 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 48 ASP cc_start: 0.7945 (t70) cc_final: 0.7686 (t0) REVERT: C 94 CYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7112 (p) REVERT: C 186 TYR cc_start: 0.8676 (p90) cc_final: 0.8185 (p90) REVERT: F 108 ARG cc_start: 0.8677 (ptp-170) cc_final: 0.8197 (ptp-170) REVERT: F 115 TYR cc_start: 0.7819 (p90) cc_final: 0.7345 (p90) REVERT: G 104 MET cc_start: 0.0979 (mmp) cc_final: 0.0609 (mmp) REVERT: I 51 SER cc_start: 0.8124 (t) cc_final: 0.7831 (p) REVERT: I 54 TYR cc_start: 0.8318 (t80) cc_final: 0.7904 (t80) REVERT: I 111 TYR cc_start: 0.8069 (m-80) cc_final: 0.7813 (m-80) REVERT: L 50 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8297 (mmtt) REVERT: b 67 MET cc_start: 0.4921 (ptm) cc_final: 0.4270 (ptt) REVERT: f 42 MET cc_start: 0.2114 (OUTLIER) cc_final: 0.1873 (mpp) REVERT: g 41 MET cc_start: 0.3472 (mtt) cc_final: 0.3073 (ptp) REVERT: g 54 MET cc_start: -0.1419 (ttp) cc_final: -0.1828 (mtp) REVERT: i 39 MET cc_start: -0.0050 (tpt) cc_final: -0.0300 (tpp) REVERT: i 43 MET cc_start: 0.5868 (mmm) cc_final: 0.5501 (tpp) REVERT: k 25 VAL cc_start: -0.1266 (OUTLIER) cc_final: -0.1591 (m) outliers start: 100 outliers final: 66 residues processed: 482 average time/residue: 0.5576 time to fit residues: 448.9495 Evaluate side-chains 461 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 387 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 137 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain j residue 75 GLU Chi-restraints excluded: chain k residue 25 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 30.0000 chunk 268 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 352 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 404 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 425 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN K 29 ASN K 89 ASN b 158 HIS ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45168 Z= 0.272 Angle : 0.544 9.081 62256 Z= 0.277 Chirality : 0.042 0.188 7103 Planarity : 0.004 0.042 7060 Dihedral : 18.089 179.010 9093 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 13.97 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4687 helix: 0.96 (0.14), residues: 1448 sheet: -1.37 (0.17), residues: 784 loop : -0.65 (0.13), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS A 685 PHE 0.023 0.001 PHE b 106 TYR 0.023 0.001 TYR B 785 ARG 0.006 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 417 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7769 (pm20) cc_final: 0.7510 (pm20) REVERT: A 524 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7105 (mtp) REVERT: A 593 SER cc_start: 0.8720 (m) cc_final: 0.8440 (p) REVERT: A 711 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 1130 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 1351 ASP cc_start: 0.7231 (m-30) cc_final: 0.6718 (m-30) REVERT: A 1412 MET cc_start: 0.8375 (tmm) cc_final: 0.7875 (tmm) REVERT: B 93 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 124 LEU cc_start: 0.8366 (tp) cc_final: 0.8164 (tp) REVERT: B 187 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 438 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.6955 (ptm160) REVERT: B 456 GLN cc_start: 0.7655 (tt0) cc_final: 0.7223 (tt0) REVERT: B 494 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8109 (tmtt) REVERT: B 785 TYR cc_start: 0.8667 (t80) cc_final: 0.8435 (t80) REVERT: B 847 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8668 (ttmt) REVERT: B 864 ASP cc_start: 0.7321 (t0) cc_final: 0.6905 (m-30) REVERT: C 48 ASP cc_start: 0.7973 (t70) cc_final: 0.7727 (t0) REVERT: C 94 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7188 (p) REVERT: F 108 ARG cc_start: 0.8716 (ptp-170) cc_final: 0.8173 (ptp-170) REVERT: F 115 TYR cc_start: 0.7746 (p90) cc_final: 0.7314 (p90) REVERT: I 51 SER cc_start: 0.8109 (t) cc_final: 0.7861 (p) REVERT: I 54 TYR cc_start: 0.8339 (t80) cc_final: 0.7895 (t80) REVERT: K 37 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7836 (ptpt) REVERT: L 27 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6757 (tm-30) REVERT: L 50 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8193 (mmtt) REVERT: b 67 MET cc_start: 0.5192 (ptm) cc_final: 0.4604 (ptt) REVERT: b 157 MET cc_start: 0.7158 (ppp) cc_final: 0.6816 (ptm) REVERT: f 42 MET cc_start: 0.2221 (OUTLIER) cc_final: 0.1063 (pmm) REVERT: g 41 MET cc_start: 0.3345 (mtt) cc_final: 0.2967 (ptp) REVERT: h 62 ILE cc_start: 0.0003 (OUTLIER) cc_final: -0.0413 (pt) REVERT: i 43 MET cc_start: 0.6086 (mmm) cc_final: 0.5697 (tpp) REVERT: k 25 VAL cc_start: -0.1391 (OUTLIER) cc_final: -0.1702 (m) outliers start: 115 outliers final: 75 residues processed: 498 average time/residue: 0.5410 time to fit residues: 448.6898 Evaluate side-chains 475 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 392 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 137 SER Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain h residue 62 ILE Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 75 GLU Chi-restraints excluded: chain k residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 5.9990 chunk 426 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 474 optimal weight: 4.9990 chunk 393 optimal weight: 50.0000 chunk 219 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 930 GLN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN K 89 ASN b 158 HIS ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45168 Z= 0.191 Angle : 0.517 10.895 62256 Z= 0.262 Chirality : 0.041 0.192 7103 Planarity : 0.003 0.042 7060 Dihedral : 18.057 179.790 9093 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.33 % Allowed : 14.92 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4687 helix: 1.16 (0.14), residues: 1444 sheet: -1.17 (0.18), residues: 776 loop : -0.52 (0.13), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.004 0.001 HIS A1044 PHE 0.024 0.001 PHE b 106 TYR 0.019 0.001 TYR B 262 ARG 0.006 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 421 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7689 (pm20) cc_final: 0.7396 (pm20) REVERT: A 524 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7081 (mtp) REVERT: A 593 SER cc_start: 0.8690 (m) cc_final: 0.8385 (p) REVERT: A 711 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 899 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: A 1035 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7551 (mp0) REVERT: A 1351 ASP cc_start: 0.7208 (m-30) cc_final: 0.6669 (m-30) REVERT: A 1412 MET cc_start: 0.8353 (tmm) cc_final: 0.7835 (tmm) REVERT: B 93 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7793 (tp) REVERT: B 187 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 264 LYS cc_start: 0.8586 (pptt) cc_final: 0.8270 (ptpp) REVERT: B 456 GLN cc_start: 0.7568 (tt0) cc_final: 0.7163 (tt0) REVERT: B 494 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8163 (tmtt) REVERT: B 847 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8686 (ttmt) REVERT: B 864 ASP cc_start: 0.7293 (t0) cc_final: 0.6869 (m-30) REVERT: C 48 ASP cc_start: 0.7949 (t70) cc_final: 0.7701 (t0) REVERT: C 66 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8016 (t70) REVERT: C 94 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7137 (p) REVERT: C 246 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8904 (mm) REVERT: F 108 ARG cc_start: 0.8657 (ptp-170) cc_final: 0.7957 (ptp-170) REVERT: F 115 TYR cc_start: 0.7726 (p90) cc_final: 0.7348 (p90) REVERT: I 51 SER cc_start: 0.8077 (t) cc_final: 0.7842 (p) REVERT: I 54 TYR cc_start: 0.8323 (t80) cc_final: 0.7930 (t80) REVERT: K 81 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7842 (t80) REVERT: L 27 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6851 (tm-30) REVERT: L 50 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8196 (mmtt) REVERT: b 49 GLU cc_start: 0.6366 (tt0) cc_final: 0.6044 (pm20) REVERT: b 67 MET cc_start: 0.5187 (ptm) cc_final: 0.4605 (ptt) REVERT: b 155 ARG cc_start: 0.8221 (tmt-80) cc_final: 0.7871 (tpt-90) REVERT: g 41 MET cc_start: 0.3405 (mtt) cc_final: 0.2999 (ptp) REVERT: i 43 MET cc_start: 0.6208 (mmm) cc_final: 0.5815 (tpp) REVERT: k 25 VAL cc_start: -0.1233 (OUTLIER) cc_final: -0.1543 (m) outliers start: 98 outliers final: 67 residues processed: 493 average time/residue: 0.5336 time to fit residues: 441.2878 Evaluate side-chains 466 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 390 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 137 SER Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 75 GLU Chi-restraints excluded: chain k residue 8 MET Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 270 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 399 optimal weight: 50.0000 chunk 264 optimal weight: 6.9990 chunk 472 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 320 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN K 29 ASN b 158 HIS ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 45168 Z= 0.419 Angle : 0.622 11.463 62256 Z= 0.316 Chirality : 0.044 0.191 7103 Planarity : 0.004 0.046 7060 Dihedral : 18.150 178.975 9093 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.66 % Allowed : 15.82 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4687 helix: 0.86 (0.14), residues: 1445 sheet: -1.39 (0.17), residues: 783 loop : -0.60 (0.13), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 506 HIS 0.006 0.001 HIS B 970 PHE 0.024 0.002 PHE b 106 TYR 0.018 0.002 TYR E 8 ARG 0.008 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 405 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7786 (pm20) cc_final: 0.7518 (pm20) REVERT: A 524 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7061 (mtp) REVERT: A 593 SER cc_start: 0.8846 (m) cc_final: 0.8604 (p) REVERT: A 711 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 1351 ASP cc_start: 0.7233 (m-30) cc_final: 0.6711 (m-30) REVERT: A 1412 MET cc_start: 0.8403 (tmm) cc_final: 0.7896 (tmm) REVERT: B 48 ASP cc_start: 0.7703 (m-30) cc_final: 0.7481 (m-30) REVERT: B 93 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7907 (tp) REVERT: B 187 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 438 ARG cc_start: 0.7370 (ttp-110) cc_final: 0.7063 (ptm160) REVERT: B 456 GLN cc_start: 0.7746 (tt0) cc_final: 0.7274 (tt0) REVERT: B 494 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8261 (tmtt) REVERT: B 847 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8820 (ttmt) REVERT: B 864 ASP cc_start: 0.7505 (t0) cc_final: 0.7057 (m-30) REVERT: B 1037 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 1166 SER cc_start: 0.8841 (m) cc_final: 0.8519 (p) REVERT: C 48 ASP cc_start: 0.8090 (t70) cc_final: 0.7845 (t0) REVERT: C 66 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8067 (t70) REVERT: C 94 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7109 (p) REVERT: C 246 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8970 (mm) REVERT: E 177 ASP cc_start: 0.8483 (t70) cc_final: 0.8198 (t0) REVERT: F 61 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7933 (mt-10) REVERT: F 108 ARG cc_start: 0.8744 (ptp-170) cc_final: 0.7936 (ptp-170) REVERT: F 115 TYR cc_start: 0.7743 (p90) cc_final: 0.7288 (p90) REVERT: I 51 SER cc_start: 0.8080 (t) cc_final: 0.7810 (p) REVERT: I 54 TYR cc_start: 0.8507 (t80) cc_final: 0.8100 (t80) REVERT: I 125 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6573 (mm-30) REVERT: J 14 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9023 (t) REVERT: K 81 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8038 (t80) REVERT: L 50 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8229 (mmtt) REVERT: b 49 GLU cc_start: 0.6338 (tt0) cc_final: 0.6059 (pm20) REVERT: b 67 MET cc_start: 0.5525 (ptm) cc_final: 0.4938 (ptt) REVERT: c 82 MET cc_start: -0.0373 (mmt) cc_final: -0.0766 (mmt) REVERT: g 41 MET cc_start: 0.2951 (mtt) cc_final: 0.2634 (ptp) REVERT: i 39 MET cc_start: -0.1250 (tpt) cc_final: -0.1632 (tpp) REVERT: i 43 MET cc_start: 0.6329 (mmm) cc_final: 0.5381 (tpp) REVERT: k 25 VAL cc_start: -0.1244 (OUTLIER) cc_final: -0.1548 (m) outliers start: 112 outliers final: 78 residues processed: 483 average time/residue: 0.5355 time to fit residues: 435.4622 Evaluate side-chains 472 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 384 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 137 SER Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain k residue 8 MET Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 321 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 371 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN H 126 GLN I 32 ASN K 29 ASN ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45168 Z= 0.169 Angle : 0.523 9.810 62256 Z= 0.266 Chirality : 0.041 0.227 7103 Planarity : 0.004 0.038 7060 Dihedral : 18.096 179.902 9093 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 16.87 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 4687 helix: 1.19 (0.14), residues: 1449 sheet: -1.19 (0.18), residues: 768 loop : -0.42 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 236 HIS 0.004 0.001 HIS A1397 PHE 0.021 0.001 PHE b 106 TYR 0.022 0.001 TYR b 161 ARG 0.011 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 399 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 524 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7239 (mtm) REVERT: A 593 SER cc_start: 0.8713 (m) cc_final: 0.8423 (p) REVERT: A 711 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 899 GLU cc_start: 0.7684 (mp0) cc_final: 0.7279 (mp0) REVERT: A 1351 ASP cc_start: 0.7155 (m-30) cc_final: 0.6669 (m-30) REVERT: A 1412 MET cc_start: 0.8466 (tmm) cc_final: 0.7937 (tmm) REVERT: B 93 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7758 (tp) REVERT: B 438 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6826 (ptm160) REVERT: B 456 GLN cc_start: 0.7538 (tt0) cc_final: 0.7049 (tt0) REVERT: B 494 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8288 (tmtt) REVERT: B 847 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8697 (ttmt) REVERT: B 864 ASP cc_start: 0.7310 (t0) cc_final: 0.6903 (m-30) REVERT: C 48 ASP cc_start: 0.7969 (t70) cc_final: 0.7760 (t0) REVERT: C 66 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.7874 (t70) REVERT: C 94 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7101 (p) REVERT: C 246 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8855 (mm) REVERT: E 177 ASP cc_start: 0.8484 (t70) cc_final: 0.8148 (t0) REVERT: F 61 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7892 (mt-10) REVERT: F 108 ARG cc_start: 0.8679 (ptp-170) cc_final: 0.7977 (ptp-170) REVERT: F 115 TYR cc_start: 0.7685 (p90) cc_final: 0.7362 (p90) REVERT: I 51 SER cc_start: 0.8050 (t) cc_final: 0.7819 (p) REVERT: I 54 TYR cc_start: 0.8317 (t80) cc_final: 0.7940 (t80) REVERT: I 109 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: K 81 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7809 (t80) REVERT: L 50 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8295 (mmtt) REVERT: b 49 GLU cc_start: 0.6438 (tt0) cc_final: 0.6115 (pm20) REVERT: b 67 MET cc_start: 0.5588 (ptm) cc_final: 0.5333 (ptp) REVERT: b 155 ARG cc_start: 0.8193 (tmt-80) cc_final: 0.7923 (tpt-90) REVERT: g 41 MET cc_start: 0.2994 (mtt) cc_final: 0.2662 (ptp) REVERT: i 39 MET cc_start: -0.1140 (tpt) cc_final: -0.1445 (tpp) REVERT: i 43 MET cc_start: 0.6216 (mmm) cc_final: 0.5843 (tpp) REVERT: k 25 VAL cc_start: -0.1315 (OUTLIER) cc_final: -0.1618 (m) outliers start: 73 outliers final: 53 residues processed: 448 average time/residue: 0.5571 time to fit residues: 416.1533 Evaluate side-chains 448 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 387 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain k residue 8 MET Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 3.9990 chunk 452 optimal weight: 7.9990 chunk 412 optimal weight: 0.8980 chunk 440 optimal weight: 50.0000 chunk 264 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 345 optimal weight: 0.0770 chunk 135 optimal weight: 0.9990 chunk 397 optimal weight: 30.0000 chunk 416 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN K 89 ASN ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45168 Z= 0.180 Angle : 0.519 9.903 62256 Z= 0.263 Chirality : 0.041 0.199 7103 Planarity : 0.003 0.040 7060 Dihedral : 18.049 179.826 9093 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.78 % Allowed : 17.11 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.13), residues: 4687 helix: 1.30 (0.14), residues: 1457 sheet: -1.12 (0.18), residues: 768 loop : -0.33 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 22 HIS 0.005 0.001 HIS B 939 PHE 0.022 0.001 PHE b 106 TYR 0.027 0.001 TYR b 161 ARG 0.010 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 398 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7372 (mtm) REVERT: A 593 SER cc_start: 0.8668 (m) cc_final: 0.8362 (p) REVERT: A 711 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 899 GLU cc_start: 0.7809 (mp0) cc_final: 0.7383 (mp0) REVERT: A 1351 ASP cc_start: 0.7097 (m-30) cc_final: 0.6643 (m-30) REVERT: A 1412 MET cc_start: 0.8400 (tmm) cc_final: 0.7837 (tmm) REVERT: B 93 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 187 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8735 (mm) REVERT: B 438 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6795 (ptm160) REVERT: B 456 GLN cc_start: 0.7503 (tt0) cc_final: 0.7027 (tt0) REVERT: B 494 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8279 (tmtt) REVERT: B 847 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8700 (ttmt) REVERT: B 864 ASP cc_start: 0.7436 (t0) cc_final: 0.7025 (m-30) REVERT: B 1166 SER cc_start: 0.8693 (m) cc_final: 0.8344 (p) REVERT: C 48 ASP cc_start: 0.7996 (t70) cc_final: 0.7787 (t0) REVERT: C 66 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.7880 (t70) REVERT: C 94 CYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6968 (p) REVERT: F 108 ARG cc_start: 0.8622 (ptp-170) cc_final: 0.7758 (ptp-170) REVERT: F 115 TYR cc_start: 0.7634 (p90) cc_final: 0.7302 (p90) REVERT: G 104 MET cc_start: 0.0898 (mmp) cc_final: 0.0611 (mmp) REVERT: I 51 SER cc_start: 0.8015 (t) cc_final: 0.7801 (p) REVERT: I 54 TYR cc_start: 0.8329 (t80) cc_final: 0.8002 (t80) REVERT: I 109 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8027 (ttm-80) REVERT: K 81 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7831 (t80) REVERT: L 50 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8285 (mmtt) REVERT: b 49 GLU cc_start: 0.6470 (tt0) cc_final: 0.6129 (pm20) REVERT: b 67 MET cc_start: 0.5689 (ptm) cc_final: 0.5069 (ptt) REVERT: b 155 ARG cc_start: 0.8151 (tmt-80) cc_final: 0.7914 (tpt-90) REVERT: f 14 LEU cc_start: -0.4305 (OUTLIER) cc_final: -0.4545 (tp) REVERT: g 41 MET cc_start: 0.3099 (mtt) cc_final: 0.2762 (ptp) REVERT: i 39 MET cc_start: -0.0845 (tpt) cc_final: -0.1161 (tpp) REVERT: i 43 MET cc_start: 0.6219 (mmm) cc_final: 0.5826 (tpp) REVERT: k 25 VAL cc_start: -0.1447 (OUTLIER) cc_final: -0.1764 (m) outliers start: 75 outliers final: 60 residues processed: 445 average time/residue: 0.5309 time to fit residues: 399.6872 Evaluate side-chains 457 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 389 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain k residue 8 MET Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 30.0000 chunk 465 optimal weight: 0.0770 chunk 284 optimal weight: 20.0000 chunk 220 optimal weight: 0.6980 chunk 323 optimal weight: 4.9990 chunk 488 optimal weight: 8.9990 chunk 449 optimal weight: 20.0000 chunk 388 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 300 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS A 783 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN K 29 ASN K 89 ASN ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45168 Z= 0.250 Angle : 0.544 10.189 62256 Z= 0.275 Chirality : 0.042 0.201 7103 Planarity : 0.004 0.042 7060 Dihedral : 18.055 179.437 9093 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.73 % Allowed : 17.30 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4687 helix: 1.29 (0.14), residues: 1450 sheet: -1.16 (0.18), residues: 775 loop : -0.33 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 236 HIS 0.004 0.001 HIS A 685 PHE 0.023 0.001 PHE b 106 TYR 0.013 0.001 TYR E 26 ARG 0.009 0.000 ARG A 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 393 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7262 (mtm) REVERT: A 593 SER cc_start: 0.8746 (m) cc_final: 0.8469 (p) REVERT: A 711 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 899 GLU cc_start: 0.7741 (mp0) cc_final: 0.7303 (mp0) REVERT: A 986 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6680 (mtm) REVERT: A 1351 ASP cc_start: 0.7148 (m-30) cc_final: 0.6690 (m-30) REVERT: A 1412 MET cc_start: 0.8401 (tmm) cc_final: 0.7784 (tmm) REVERT: A 1414 ILE cc_start: 0.8737 (mm) cc_final: 0.8370 (mm) REVERT: B 93 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 187 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8758 (mm) REVERT: B 438 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6905 (ptm160) REVERT: B 456 GLN cc_start: 0.7561 (tt0) cc_final: 0.7108 (tt0) REVERT: B 494 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8294 (tmtt) REVERT: B 847 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8684 (ttmt) REVERT: B 864 ASP cc_start: 0.7486 (t0) cc_final: 0.7106 (m-30) REVERT: B 1166 SER cc_start: 0.8698 (m) cc_final: 0.8364 (p) REVERT: C 48 ASP cc_start: 0.8040 (t70) cc_final: 0.7801 (t0) REVERT: C 66 HIS cc_start: 0.8848 (OUTLIER) cc_final: 0.7954 (t70) REVERT: C 94 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6999 (p) REVERT: E 177 ASP cc_start: 0.8499 (t70) cc_final: 0.8195 (t0) REVERT: F 108 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.7720 (ptp-170) REVERT: F 115 TYR cc_start: 0.7609 (p90) cc_final: 0.7278 (p90) REVERT: G 104 MET cc_start: 0.0753 (mmp) cc_final: 0.0455 (mmp) REVERT: I 51 SER cc_start: 0.8069 (t) cc_final: 0.7826 (p) REVERT: I 54 TYR cc_start: 0.8424 (t80) cc_final: 0.8036 (t80) REVERT: I 109 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.7997 (ttm-80) REVERT: K 81 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7852 (t80) REVERT: L 50 LYS cc_start: 0.8665 (mmpt) cc_final: 0.8320 (mmtt) REVERT: b 49 GLU cc_start: 0.6358 (tt0) cc_final: 0.6088 (pm20) REVERT: b 67 MET cc_start: 0.5961 (ptm) cc_final: 0.5258 (ptt) REVERT: b 155 ARG cc_start: 0.8143 (tmt-80) cc_final: 0.7937 (tpt-90) REVERT: c 82 MET cc_start: -0.0150 (mmt) cc_final: -0.0377 (mmt) REVERT: f 14 LEU cc_start: -0.4256 (OUTLIER) cc_final: -0.4529 (tp) REVERT: g 41 MET cc_start: 0.3092 (mtt) cc_final: 0.2753 (ptp) REVERT: i 39 MET cc_start: -0.0925 (tpt) cc_final: -0.1230 (tpp) REVERT: i 43 MET cc_start: 0.6254 (mmm) cc_final: 0.5857 (tpp) REVERT: k 25 VAL cc_start: -0.1409 (OUTLIER) cc_final: -0.1706 (t) outliers start: 73 outliers final: 59 residues processed: 440 average time/residue: 0.5605 time to fit residues: 414.2848 Evaluate side-chains 454 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 386 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain k residue 8 MET Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 389 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 399 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B1145 GLN K 29 ASN ** e 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.196055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.143961 restraints weight = 67153.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.139239 restraints weight = 77915.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.142234 restraints weight = 64897.533| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 45168 Z= 0.319 Angle : 0.578 10.430 62256 Z= 0.293 Chirality : 0.043 0.202 7103 Planarity : 0.004 0.044 7060 Dihedral : 18.097 178.827 9093 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.95 % Allowed : 17.37 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4687 helix: 1.18 (0.14), residues: 1443 sheet: -1.23 (0.18), residues: 772 loop : -0.37 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 236 HIS 0.003 0.001 HIS B 387 PHE 0.021 0.001 PHE b 106 TYR 0.020 0.002 TYR C 208 ARG 0.009 0.000 ARG J 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9618.13 seconds wall clock time: 174 minutes 19.81 seconds (10459.81 seconds total)